npm - jbrowse-plugin-graphgenomeviewer - Versions diffs - 4.0.3 → 4.0.5 - Mend

jbrowse-plugin-graphgenomeviewer 4.0.3 → 4.0.5

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Files changed (27) hide show

package/dist/chunks/AddTrackWorkflow-I4EPGFPJ.js ADDED Viewed

	@@ -0,0 +1,2 @@
1	+ import{a as z}from"./chunk-FCWXYIFC.js";import{a as $}from"./chunk-D7XFR2IV.js";import{a as H}from"./chunk-J4OLMLS5.js";import{a as x,b as j,c as O,d as J,e as U}from"./chunk-XEJ47DLD.js";import{a as W,b as r}from"./chunk-FY3BTKY4.js";var C=W((Z,T)=>{T.exports=JBrowseExports["@jbrowse/core/util/tss-react"]});var c=r(U(),1),p=r(J(),1),m=r(H(),1),B=r(C(),1),E=r(z(),1),i=r(O(),1),P=r(j(),1);var b=r($(),1),G={RgfaTabixAdapter:"rGFA segments (tabix BED pair)",MinigraphBubbleAdapter:"Minigraph bubbles (tabix BED)"},S={RgfaTabixAdapter:"Path to segments BED (.segs.bed.gz from build_rgfa_tabix.sh; the .links.bed.gz and both .tbi are assumed beside it)",MinigraphBubbleAdapter:"Path to bubbles BED (.bed.gz from gfatools bubble; the .tbi is assumed beside it)"},u=".segs.bed.gz";function f(t){return"uri"in t?t.uri:"localPath"in t?t.localPath:""}function X(t){let e=f(t);if(!e.endsWith(u))throw new Error(`Expected a segments BED ending in ${u}, got ${e\|\|"a blob"}`);let a=`${e.slice(0,-u.length)}.links.bed.gz`;return"uri"in t?{...t,uri:a}:"localPath"in t?{...t,localPath:a}:t}function A(t,e){return e?{location:e,indexType:(0,b.makeIndexType)(f(e),"CSI","TBI")}:{location:(0,b.makeIndex)(t,".tbi"),indexType:"TBI"}}function q(t,e){return e!==void 0&&f(e).endsWith(".csi")?{location:(0,b.makeIndex)(t,".csi"),indexType:"CSI"}:{location:(0,b.makeIndex)(t,".tbi"),indexType:"TBI"}}function I(t,e){let a=e.trim();return a?{assemblyNameToPanSN:{[t]:a}}:{}}function K({choice:t,loc:e,indexLoc:a,assembly:s,sample:l}){if(t==="MinigraphBubbleAdapter")return{type:"MinigraphBubbleAdapter",bubblesLocation:e,index:A(e,a),...I(s,l)};let d=X(e);return{type:"RgfaTabixAdapter",segmentsLocation:e,segmentsIndex:A(e,a),linksLocation:d,linksIndex:q(d,a),...I(s,l)}}function R(t){let{choice:e,assembly:a,trackId:s,name:l}=t;return{type:"FeatureTrack",trackId:s,name:l,assemblyNames:[a],adapter:K(t),...e==="RgfaTabixAdapter"?{displays:[{type:"LinearGraphDisplay",displayId:`${s}-LinearGraphDisplay`},{type:"LinearBasicDisplay",displayId:`${s}-LinearBasicDisplay`}],displayDefaults:{showLabels:"none"}}:{}}}var n=r(x(),1),Q=(0,B.makeStyles)()(t=>({paper:{margin:t.spacing(),padding:t.spacing()},field:{marginTop:t.spacing(2)},submit:{marginTop:25,marginBottom:100,display:"block"}})),V=["RgfaTabixAdapter","MinigraphBubbleAdapter"],Y=(0,P.observer)(function({model:e}){let{classes:a}=Q(),s=(0,m.getSession)(e),l=(0,E.getRoot)(e),[d,M]=(0,c.useState)("RgfaTabixAdapter"),[h,N]=(0,c.useState)(),[y,D]=(0,c.useState)(),[F,v]=(0,c.useState)(""),[g,w]=(0,c.useState)("Pangenome graph"),[L,k]=(0,c.useState)();function _(){if(!(!h\|\|!e.assembly))try{k(void 0);let o=g.trim();(0,m.addTrackFromWidget)({model:e,session:s,conf:R({choice:d,loc:h,indexLoc:y,assembly:e.assembly,sample:F,trackId:(0,m.makeTrackId)({name:o}),name:o})})}catch(o){k(o)}}return(0,n.jsxs)(i.Paper,{className:a.paper,children:[L?(0,n.jsx)(p.ErrorMessage,{error:L}):null,(0,n.jsxs)(i.FormControl,{children:[(0,n.jsx)(i.FormLabel,{children:"File type"}),(0,n.jsx)(i.RadioGroup,{value:d,onChange:o=>{M(o.target.value)},children:V.map(o=>(0,n.jsx)(i.FormControlLabel,{value:o,control:(0,n.jsx)(i.Radio,{}),label:G[o]},o))})]}),(0,n.jsx)(p.FileSelector,{location:h,name:S[d],rootModel:l,setLocation:N}),(0,n.jsx)(p.FileSelector,{location:y,name:"Path to tabix index (optional; the sibling .tbi is assumed, a .csi is recognised by name)",rootModel:l,setLocation:D}),(0,n.jsx)(i.TextField,{className:a.field,value:F,onChange:o=>{v(o.target.value)},label:"Sample name in the graph",slotProps:{htmlInput:{"data-testid":"graph-sample-input"}},helperText:"Optional. The PanSN prefix the graph gives this assembly, e.g. GRCh38 for HPRC's GRCh38#0#chr1; leave blank when the graph's stable names are bare",placeholder:"GRCh38",fullWidth:!0}),(0,n.jsx)(i.TextField,{className:a.field,value:g,helperText:"Track name",slotProps:{htmlInput:{"data-testid":"graph-track-name-input"}},onChange:o=>{w(o.target.value)}}),(0,n.jsx)(p.AssemblySelector,{session:s,helperText:"Select assembly to add track to",selected:e.assembly,onChange:o=>{e.setAssembly(o)},fullWidth:!0}),(0,n.jsx)(i.Button,{variant:"contained",className:a.submit,disabled:!h\|\|!g.trim()\|\|!e.assembly,onClick:_,children:"Submit"})]})}),ae=Y;export{ae as default};
2	+ //# sourceMappingURL=AddTrackWorkflow-I4EPGFPJ.js.map

package/dist/chunks/{AddTrackWorkflow-TPCKXM2H.js.map → AddTrackWorkflow-I4EPGFPJ.js.map} RENAMED Viewed

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["global-externals:@jbrowse/core/util/tss-react", "../../src/GraphAddTrackWorkflow/AddTrackWorkflow.tsx", "../../src/GraphAddTrackWorkflow/buildTrackConfig.ts"],
-  "sourcesContent": ["module.exports = JBrowseExports[\"@jbrowse/core/util/tss-react\"];", "import { useState } from 'react'\n\nimport { AssemblySelector, ErrorMessage, FileSelector } from '@jbrowse/core/ui'\nimport { addTrackFromWidget, getSession, makeTrackId } from '@jbrowse/core/util'\nimport { makeStyles } from '@jbrowse/core/util/tss-react'\nimport { getRoot } from '@jbrowse/mobx-state-tree'\nimport {\n  Button,\n  FormControl,\n  FormControlLabel,\n  FormLabel,\n  Paper,\n  Radio,\n  RadioGroup,\n  TextField,\n} from '@mui/material'\nimport { observer } from 'mobx-react'\n\nimport {\n  GRAPH_FILE_FIELDS,\n  GRAPH_FILE_LABELS,\n  buildTrackConfig,\n} from './buildTrackConfig'\n\nimport type { GraphFileChoice } from './buildTrackConfig'\nimport type {\n  AbstractRootModel,\n  AddTrackWorkflowModel,\n  FileLocation,\n} from '@jbrowse/core/util'\n\nconst useStyles = makeStyles()(theme => ({\n  paper: {\n    margin: theme.spacing(),\n    padding: theme.spacing(),\n  },\n  field: {\n    marginTop: theme.spacing(2),\n  },\n  submit: {\n    marginTop: 25,\n    marginBottom: 100,\n    display: 'block',\n  },\n}))\n\nconst CHOICES: GraphFileChoice[] = [\n  'RgfaTabixAdapter',\n  'MinigraphBubbleAdapter',\n]\n\nconst GraphAddTrackWidget = observer(function GraphAddTrackWidget({\n  model,\n}: {\n  model: AddTrackWorkflowModel\n}) {\n  const { classes } = useStyles()\n  const session = getSession(model)\n  const rootModel = getRoot<AbstractRootModel>(model)\n  const [choice, setChoice] = useState<GraphFileChoice>('RgfaTabixAdapter')\n  const [loc, setLoc] = useState<FileLocation>()\n  const [indexLoc, setIndexLoc] = useState<FileLocation>()\n  const [sample, setSample] = useState('')\n  const [trackName, setTrackName] = useState('Pangenome graph')\n  const [error, setError] = useState<unknown>()\n\n  function handleSubmit() {\n    if (!loc || !model.assembly) {\n      return\n    }\n    try {\n      setError(undefined)\n      const name = trackName.trim()\n      addTrackFromWidget({\n        model,\n        session,\n        conf: buildTrackConfig({\n          choice,\n          loc,\n          indexLoc,\n          assembly: model.assembly,\n          sample,\n          trackId: makeTrackId({ name }),\n          name,\n        }),\n      })\n    } catch (e) {\n      setError(e)\n    }\n  }\n\n  return (\n    <Paper className={classes.paper}>\n      {error ? <ErrorMessage error={error} /> : null}\n      <FormControl>\n        <FormLabel>File type</FormLabel>\n        <RadioGroup\n          value={choice}\n          onChange={event => {\n            setChoice(event.target.value as GraphFileChoice)\n          }}\n        >\n          {CHOICES.map(option => (\n            <FormControlLabel\n              key={option}\n              value={option}\n              control={<Radio />}\n              label={GRAPH_FILE_LABELS[option]}\n            />\n          ))}\n        </RadioGroup>\n      </FormControl>\n      <FileSelector\n        location={loc}\n        name={GRAPH_FILE_FIELDS[choice]}\n        rootModel={rootModel}\n        setLocation={setLoc}\n      />\n      <FileSelector\n        location={indexLoc}\n        name=\"Path to tabix index (optional; the sibling .tbi is assumed, a .csi is recognised by name)\"\n        rootModel={rootModel}\n        setLocation={setIndexLoc}\n      />\n      <TextField\n        className={classes.field}\n        value={sample}\n        onChange={event => {\n          setSample(event.target.value)\n        }}\n        label=\"Sample name in the graph\"\n        slotProps={{ htmlInput: { 'data-testid': 'graph-sample-input' } }}\n        helperText=\"Optional. The PanSN prefix the graph gives this assembly, e.g. GRCh38 for HPRC's GRCh38#0#chr1; leave blank when the graph's stable names are bare\"\n        placeholder=\"GRCh38\"\n        fullWidth\n      />\n      <TextField\n        className={classes.field}\n        value={trackName}\n        helperText=\"Track name\"\n        slotProps={{ htmlInput: { 'data-testid': 'graph-track-name-input' } }}\n        onChange={event => {\n          setTrackName(event.target.value)\n        }}\n      />\n      <AssemblySelector\n        session={session}\n        helperText=\"Select assembly to add track to\"\n        selected={model.assembly}\n        onChange={arg => {\n          model.setAssembly(arg)\n        }}\n        fullWidth\n      />\n      <Button\n        variant=\"contained\"\n        className={classes.submit}\n        disabled={!loc || !trackName.trim() || !model.assembly}\n        onClick={handleSubmit}\n      >\n        Submit\n      </Button>\n    </Paper>\n  )\n})\n\nexport default GraphAddTrackWidget\n", "import { makeIndex, makeIndexType } from '@jbrowse/core/util/tracks'\n\nimport type { FileLocation } from '@jbrowse/core/util'\n\nexport type GraphFileChoice = 'RgfaTabixAdapter' | 'MinigraphBubbleAdapter'\n\nexport const GRAPH_FILE_LABELS: Record<GraphFileChoice, string> = {\n  RgfaTabixAdapter: 'rGFA segments (tabix BED pair)',\n  MinigraphBubbleAdapter: 'Minigraph bubbles (tabix BED)',\n}\n\nexport const GRAPH_FILE_FIELDS: Record<GraphFileChoice, string> = {\n  RgfaTabixAdapter:\n    'Path to segments BED (.segs.bed.gz from build_rgfa_tabix.sh; the .links.bed.gz and both .tbi are assumed beside it)',\n  MinigraphBubbleAdapter:\n    'Path to bubbles BED (.bed.gz from gfatools bubble; the .tbi is assumed beside it)',\n}\n\nconst SEGMENTS_SUFFIX = '.segs.bed.gz'\n\nfunction locationName(loc: FileLocation) {\n  return 'uri' in loc ? loc.uri : 'localPath' in loc ? loc.localPath : ''\n}\n\nfunction linksLocation(loc: FileLocation) {\n  const name = locationName(loc)\n  if (!name.endsWith(SEGMENTS_SUFFIX)) {\n    throw new Error(\n      `Expected a segments BED ending in ${SEGMENTS_SUFFIX}, got ${name || 'a blob'}`,\n    )\n  }\n  const links = `${name.slice(0, -SEGMENTS_SUFFIX.length)}.links.bed.gz`\n  return 'uri' in loc\n    ? { ...loc, uri: links }\n    : 'localPath' in loc\n      ? { ...loc, localPath: links }\n      : loc\n}\n\nfunction tabixIndex(loc: FileLocation, indexLoc: FileLocation | undefined) {\n  return indexLoc\n    ? {\n        location: indexLoc,\n        indexType: makeIndexType(locationName(indexLoc), 'CSI', 'TBI'),\n      }\n    : { location: makeIndex(loc, '.tbi'), indexType: 'TBI' }\n}\n\n// The links file's index is assumed beside it, of the kind the segments' is.\nfunction siblingIndex(loc: FileLocation, indexLoc: FileLocation | undefined) {\n  const csi = indexLoc !== undefined && locationName(indexLoc).endsWith('.csi')\n  return csi\n    ? { location: makeIndex(loc, '.csi'), indexType: 'CSI' }\n    : { location: makeIndex(loc, '.tbi'), indexType: 'TBI' }\n}\n\nfunction panSN(assembly: string, sample: string) {\n  const name = sample.trim()\n  return name ? { assemblyNameToPanSN: { [assembly]: name } } : {}\n}\n\nexport function buildAdapterConfig({\n  choice,\n  loc,\n  indexLoc,\n  assembly,\n  sample,\n}: {\n  choice: GraphFileChoice\n  loc: FileLocation\n  indexLoc: FileLocation | undefined\n  assembly: string\n  sample: string\n}) {\n  if (choice === 'MinigraphBubbleAdapter') {\n    return {\n      type: 'MinigraphBubbleAdapter',\n      bubblesLocation: loc,\n      index: tabixIndex(loc, indexLoc),\n      ...panSN(assembly, sample),\n    }\n  }\n  const links = linksLocation(loc)\n  return {\n    type: 'RgfaTabixAdapter',\n    segmentsLocation: loc,\n    segmentsIndex: tabixIndex(loc, indexLoc),\n    linksLocation: links,\n    linksIndex: siblingIndex(links, indexLoc),\n    ...panSN(assembly, sample),\n  }\n}\n\nexport function buildTrackConfig(args: {\n  choice: GraphFileChoice\n  loc: FileLocation\n  indexLoc: FileLocation | undefined\n  assembly: string\n  sample: string\n  trackId: string\n  name: string\n}) {\n  const { choice, assembly, trackId, name } = args\n  return {\n    type: 'FeatureTrack',\n    trackId,\n    name,\n    assemblyNames: [assembly],\n    adapter: buildAdapterConfig(args),\n    ...(choice === 'RgfaTabixAdapter'\n      ? { displayDefaults: { showLabels: 'none' } }\n      : {}),\n  }\n}\n"],
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+  "sourcesContent": ["module.exports = JBrowseExports[\"@jbrowse/core/util/tss-react\"];", "import { useState } from 'react'\n\nimport { AssemblySelector, ErrorMessage, FileSelector } from '@jbrowse/core/ui'\nimport { addTrackFromWidget, getSession, makeTrackId } from '@jbrowse/core/util'\nimport { makeStyles } from '@jbrowse/core/util/tss-react'\nimport { getRoot } from '@jbrowse/mobx-state-tree'\nimport {\n  Button,\n  FormControl,\n  FormControlLabel,\n  FormLabel,\n  Paper,\n  Radio,\n  RadioGroup,\n  TextField,\n} from '@mui/material'\nimport { observer } from 'mobx-react'\n\nimport {\n  GRAPH_FILE_FIELDS,\n  GRAPH_FILE_LABELS,\n  buildTrackConfig,\n} from './buildTrackConfig'\n\nimport type { GraphFileChoice } from './buildTrackConfig'\nimport type {\n  AbstractRootModel,\n  AddTrackWorkflowModel,\n  FileLocation,\n} from '@jbrowse/core/util'\n\nconst useStyles = makeStyles()(theme => ({\n  paper: {\n    margin: theme.spacing(),\n    padding: theme.spacing(),\n  },\n  field: {\n    marginTop: theme.spacing(2),\n  },\n  submit: {\n    marginTop: 25,\n    marginBottom: 100,\n    display: 'block',\n  },\n}))\n\nconst CHOICES: GraphFileChoice[] = [\n  'RgfaTabixAdapter',\n  'MinigraphBubbleAdapter',\n]\n\nconst GraphAddTrackWidget = observer(function GraphAddTrackWidget({\n  model,\n}: {\n  model: AddTrackWorkflowModel\n}) {\n  const { classes } = useStyles()\n  const session = getSession(model)\n  const rootModel = getRoot<AbstractRootModel>(model)\n  const [choice, setChoice] = useState<GraphFileChoice>('RgfaTabixAdapter')\n  const [loc, setLoc] = useState<FileLocation>()\n  const [indexLoc, setIndexLoc] = useState<FileLocation>()\n  const [sample, setSample] = useState('')\n  const [trackName, setTrackName] = useState('Pangenome graph')\n  const [error, setError] = useState<unknown>()\n\n  function handleSubmit() {\n    if (!loc || !model.assembly) {\n      return\n    }\n    try {\n      setError(undefined)\n      const name = trackName.trim()\n      addTrackFromWidget({\n        model,\n        session,\n        conf: buildTrackConfig({\n          choice,\n          loc,\n          indexLoc,\n          assembly: model.assembly,\n          sample,\n          trackId: makeTrackId({ name }),\n          name,\n        }),\n      })\n    } catch (e) {\n      setError(e)\n    }\n  }\n\n  return (\n    <Paper className={classes.paper}>\n      {error ? <ErrorMessage error={error} /> : null}\n      <FormControl>\n        <FormLabel>File type</FormLabel>\n        <RadioGroup\n          value={choice}\n          onChange={event => {\n            setChoice(event.target.value as GraphFileChoice)\n          }}\n        >\n          {CHOICES.map(option => (\n            <FormControlLabel\n              key={option}\n              value={option}\n              control={<Radio />}\n              label={GRAPH_FILE_LABELS[option]}\n            />\n          ))}\n        </RadioGroup>\n      </FormControl>\n      <FileSelector\n        location={loc}\n        name={GRAPH_FILE_FIELDS[choice]}\n        rootModel={rootModel}\n        setLocation={setLoc}\n      />\n      <FileSelector\n        location={indexLoc}\n        name=\"Path to tabix index (optional; the sibling .tbi is assumed, a .csi is recognised by name)\"\n        rootModel={rootModel}\n        setLocation={setIndexLoc}\n      />\n      <TextField\n        className={classes.field}\n        value={sample}\n        onChange={event => {\n          setSample(event.target.value)\n        }}\n        label=\"Sample name in the graph\"\n        slotProps={{ htmlInput: { 'data-testid': 'graph-sample-input' } }}\n        helperText=\"Optional. The PanSN prefix the graph gives this assembly, e.g. GRCh38 for HPRC's GRCh38#0#chr1; leave blank when the graph's stable names are bare\"\n        placeholder=\"GRCh38\"\n        fullWidth\n      />\n      <TextField\n        className={classes.field}\n        value={trackName}\n        helperText=\"Track name\"\n        slotProps={{ htmlInput: { 'data-testid': 'graph-track-name-input' } }}\n        onChange={event => {\n          setTrackName(event.target.value)\n        }}\n      />\n      <AssemblySelector\n        session={session}\n        helperText=\"Select assembly to add track to\"\n        selected={model.assembly}\n        onChange={arg => {\n          model.setAssembly(arg)\n        }}\n        fullWidth\n      />\n      <Button\n        variant=\"contained\"\n        className={classes.submit}\n        disabled={!loc || !trackName.trim() || !model.assembly}\n        onClick={handleSubmit}\n      >\n        Submit\n      </Button>\n    </Paper>\n  )\n})\n\nexport default GraphAddTrackWidget\n", "import { makeIndex, makeIndexType } from '@jbrowse/core/util/tracks'\n\nimport type { FileLocation } from '@jbrowse/core/util'\n\nexport type GraphFileChoice = 'RgfaTabixAdapter' | 'MinigraphBubbleAdapter'\n\nexport const GRAPH_FILE_LABELS: Record<GraphFileChoice, string> = {\n  RgfaTabixAdapter: 'rGFA segments (tabix BED pair)',\n  MinigraphBubbleAdapter: 'Minigraph bubbles (tabix BED)',\n}\n\nexport const GRAPH_FILE_FIELDS: Record<GraphFileChoice, string> = {\n  RgfaTabixAdapter:\n    'Path to segments BED (.segs.bed.gz from build_rgfa_tabix.sh; the .links.bed.gz and both .tbi are assumed beside it)',\n  MinigraphBubbleAdapter:\n    'Path to bubbles BED (.bed.gz from gfatools bubble; the .tbi is assumed beside it)',\n}\n\nconst SEGMENTS_SUFFIX = '.segs.bed.gz'\n\nfunction locationName(loc: FileLocation) {\n  return 'uri' in loc ? loc.uri : 'localPath' in loc ? loc.localPath : ''\n}\n\nfunction linksLocation(loc: FileLocation) {\n  const name = locationName(loc)\n  if (!name.endsWith(SEGMENTS_SUFFIX)) {\n    throw new Error(\n      `Expected a segments BED ending in ${SEGMENTS_SUFFIX}, got ${name || 'a blob'}`,\n    )\n  }\n  const links = `${name.slice(0, -SEGMENTS_SUFFIX.length)}.links.bed.gz`\n  return 'uri' in loc\n    ? { ...loc, uri: links }\n    : 'localPath' in loc\n      ? { ...loc, localPath: links }\n      : loc\n}\n\nfunction tabixIndex(loc: FileLocation, indexLoc: FileLocation | undefined) {\n  return indexLoc\n    ? {\n        location: indexLoc,\n        indexType: makeIndexType(locationName(indexLoc), 'CSI', 'TBI'),\n      }\n    : { location: makeIndex(loc, '.tbi'), indexType: 'TBI' }\n}\n\n// The links file's index is assumed beside it, of the kind the segments' is.\nfunction siblingIndex(loc: FileLocation, indexLoc: FileLocation | undefined) {\n  const csi = indexLoc !== undefined && locationName(indexLoc).endsWith('.csi')\n  return csi\n    ? { location: makeIndex(loc, '.csi'), indexType: 'CSI' }\n    : { location: makeIndex(loc, '.tbi'), indexType: 'TBI' }\n}\n\nfunction panSN(assembly: string, sample: string) {\n  const name = sample.trim()\n  return name ? { assemblyNameToPanSN: { [assembly]: name } } : {}\n}\n\nexport function buildAdapterConfig({\n  choice,\n  loc,\n  indexLoc,\n  assembly,\n  sample,\n}: {\n  choice: GraphFileChoice\n  loc: FileLocation\n  indexLoc: FileLocation | undefined\n  assembly: string\n  sample: string\n}) {\n  if (choice === 'MinigraphBubbleAdapter') {\n    return {\n      type: 'MinigraphBubbleAdapter',\n      bubblesLocation: loc,\n      index: tabixIndex(loc, indexLoc),\n      ...panSN(assembly, sample),\n    }\n  }\n  const links = linksLocation(loc)\n  return {\n    type: 'RgfaTabixAdapter',\n    segmentsLocation: loc,\n    segmentsIndex: tabixIndex(loc, indexLoc),\n    linksLocation: links,\n    linksIndex: siblingIndex(links, indexLoc),\n    ...panSN(assembly, sample),\n  }\n}\n\nexport function buildTrackConfig(args: {\n  choice: GraphFileChoice\n  loc: FileLocation\n  indexLoc: FileLocation | undefined\n  assembly: string\n  sample: string\n  trackId: string\n  name: string\n}) {\n  const { choice, assembly, trackId, name } = args\n  return {\n    type: 'FeatureTrack',\n    trackId,\n    name,\n    assemblyNames: [assembly],\n    adapter: buildAdapterConfig(args),\n    ...(choice === 'RgfaTabixAdapter'\n      ? {\n          displays: [\n            {\n              type: 'LinearGraphDisplay',\n              displayId: `${trackId}-LinearGraphDisplay`,\n            },\n            {\n              type: 'LinearBasicDisplay',\n              displayId: `${trackId}-LinearBasicDisplay`,\n            },\n          ],\n          displayDefaults: { showLabels: 'none' },\n        }\n      : {}),\n  }\n}\n"],
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   "names": ["require_tss_react", "__commonJSMin", "exports", "module", "import_react", "import_ui", "import_util", "import_tss_react", "import_mobx_state_tree", "import_material", "import_mobx_react", "import_tracks", "GRAPH_FILE_LABELS", "GRAPH_FILE_FIELDS", "SEGMENTS_SUFFIX", "locationName", "loc", "linksLocation", "name", "links", "tabixIndex", "indexLoc", "siblingIndex", "panSN", "assembly", "sample", "buildAdapterConfig", "choice", "buildTrackConfig", "args", "trackId", "import_jsx_runtime", "useStyles", "theme", "CHOICES", "GraphAddTrackWidget", "model", "classes", "session", "rootModel", "choice", "setChoice", "loc", "setLoc", "indexLoc", "setIndexLoc", "sample", "setSample", "trackName", "setTrackName", "error", "setError", "handleSubmit", "name", "buildTrackConfig", "e", "event", "option", "GRAPH_FILE_LABELS", "GRAPH_FILE_FIELDS", "arg", "AddTrackWorkflow_default"]
 }

package/dist/chunks/{GraphGenomeView-WPKSNN4I.js → GraphGenomeView-BQYWWF6Z.js} RENAMED Viewed

@@ -1,4 +1,4 @@
-import{a as h,b as d}from"./chunk-SDTCVLC3.js";import"./chunk-A4ZWFDQY.js";import"./chunk-ZNGDWZ6Z.js";import"./chunk-OHT6UX4C.js";import{F as M}from"./chunk-OP7IRVG6.js";import"./chunk-F4C3BEPV.js";import{a as p,b as c,c as F,d as A,e as E}from"./chunk-XEJ47DLD.js";import{b as a}from"./chunk-FY3BTKY4.js";var x=a(c(),1);var u=a(E(),1),g=a(A(),1),o=a(F(),1),G=a(c(),1),v=a(M(),1),t=a(p(),1),T=`H	VN:Z:1.0
+import{a as h,b as d}from"./chunk-RSAY56Y4.js";import"./chunk-5WJPRX4N.js";import"./chunk-ZNGDWZ6Z.js";import"./chunk-OHT6UX4C.js";import{F as M}from"./chunk-OP7IRVG6.js";import"./chunk-F4C3BEPV.js";import{a as p,b as c,c as F,d as A,e as E}from"./chunk-XEJ47DLD.js";import{b as a}from"./chunk-FY3BTKY4.js";var x=a(c(),1);var u=a(E(),1),g=a(A(),1),o=a(F(),1),G=a(c(),1),v=a(M(),1),t=a(p(),1),T=`H	VN:Z:1.0
 S	1	ACGT
 S	2	GGCC
 S	3	TTAA
@@ -7,4 +7,4 @@ L	1	+	2	+	0M
 L	1	+	3	+	0M
 L	2	+	4	+	0M
 L	3	+	4	+	0M`,N=(0,v.makeStyles)()({column:{display:"flex",flexDirection:"column",gap:8},rowEnd:{display:"flex",gap:8,alignItems:"flex-end"},rowCenter:{display:"flex",gap:8,alignItems:"center"},flex1:{flex:1},paper:{padding:16,margin:8,maxWidth:560,marginInline:"auto"},header:{marginBottom:12},footer:{marginTop:12,display:"flex",justifyContent:"flex-end"}}),S=(0,G.observer)(function({model:e}){let{classes:n}=N(),[l,L]=(0,u.useState)("");function f(){l.trim()&&e.loadGFAFromLocation({uri:l,locationType:"UriLocation"})}function w(i){let m=i.target.files?.[0];m&&m.text().then(s=>e.loadGFA(s,m.name)).catch(s=>{e.setError(s)})}return(0,t.jsxs)(o.Paper,{className:n.paper,children:[(0,t.jsx)("div",{className:n.header,children:(0,t.jsx)(o.Typography,{variant:"h6",children:"Load a GFA graph"})}),(0,t.jsxs)("div",{className:n.column,children:[(0,t.jsxs)("div",{className:n.rowCenter,children:[(0,t.jsxs)(o.Button,{variant:"outlined",component:"label",size:"small",children:["Choose file",(0,t.jsx)("input",{type:"file",accept:".gfa,.gfa1,.gfa2",hidden:!0,onChange:i=>{w(i)}})]}),(0,t.jsx)(o.Typography,{variant:"caption",color:"text.secondary",children:"Whole-file GFA; best for small/medium graphs."})]}),(0,t.jsxs)("div",{className:n.rowEnd,children:[(0,t.jsx)(o.TextField,{size:"small",label:"URL",placeholder:"https://example.com/graph.gfa",value:l,onChange:i=>{L(i.target.value)},onKeyDown:i=>{i.key==="Enter"&&f()},className:n.flex1}),(0,t.jsx)(o.Button,{variant:"contained",onClick:()=>{f()},disabled:!l.trim(),children:"Open"})]})]}),(0,t.jsx)("div",{className:n.footer,children:(0,t.jsx)(o.Button,{size:"small",onClick:()=>{e.loadGFA(T,"Example graph")},children:"Load 4-node example"})}),e.error?(0,t.jsx)(g.ErrorBanner,{error:e.error}):null]})}),y=S;var r=a(p(),1),I=(0,x.observer)(function({model:e}){return e.hasGraph?(0,r.jsx)(h,{model:e}):e.canRetryLoad&&(e.error||e.loadCanceled)?(0,r.jsx)(d,{model:e}):(0,r.jsxs)(r.Fragment,{children:[e.isLoading?(0,r.jsx)(d,{model:e}):null,(0,r.jsx)("div",{hidden:e.isLoading,children:(0,r.jsx)(y,{model:e})})]})}),U=I;export{U as default};
-//# sourceMappingURL=GraphGenomeView-WPKSNN4I.js.map
+//# sourceMappingURL=GraphGenomeView-BQYWWF6Z.js.map

package/dist/chunks/LinearGraphDisplay-7O3VQHKU.js ADDED Viewed

	@@ -0,0 +1,2 @@
1	+ import{a as r,b as i}from"./chunk-RSAY56Y4.js";import"./chunk-5WJPRX4N.js";import"./chunk-ZNGDWZ6Z.js";import"./chunk-OHT6UX4C.js";import"./chunk-OP7IRVG6.js";import"./chunk-F4C3BEPV.js";import{a as e,b as s,c as u}from"./chunk-XEJ47DLD.js";import{b as o}from"./chunk-FY3BTKY4.js";var d=o(u(),1),n=o(s(),1);var t=o(e(),1),h={position:"absolute",left:8,top:4,zIndex:5,background:"rgba(255,255,255,0.82)",padding:"0 4px",borderRadius:3},c=(0,n.observer)(function({model:p}){let{pane:a,height:l}=p;return(0,t.jsxs)("div",{"data-testid":"linear-graph-display","data-layout":a.layoutMode,"data-cut-tier":a.cutTier,"data-recuts":a.recuts,"data-node-count":a.hasGraph?a.nodeCount:void 0,"data-loading":a.isLoading?"":void 0,style:{position:"relative",width:a.width,height:l,overflow:"hidden"},children:[(0,t.jsx)(r,{model:a,toolbar:!1}),a.hasGraph?null:(0,t.jsx)(i,{model:a}),a.cutNote?(0,t.jsx)(d.Typography,{variant:"caption",color:"warning.main",style:h,"data-testid":"graph-cut-note",children:a.cutNote}):null]})}),g=c;export{g as default};
2	+ //# sourceMappingURL=LinearGraphDisplay-7O3VQHKU.js.map

package/dist/chunks/{LinearGraphDisplay-7POYIRIB.js.map → LinearGraphDisplay-7O3VQHKU.js.map} RENAMED Viewed

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../../src/LinearGraphDisplay/components/LinearGraphDisplay.tsx"],
-  "sourcesContent": ["import { Typography } from '@mui/material'\nimport { observer } from 'mobx-react'\n\nimport GraphCanvas from '../../GraphGenomeView/components/GraphCanvas'\nimport GraphLoadStatus from '../../GraphGenomeView/components/GraphLoadStatus'\n\nimport type { LinearGraphDisplayModel } from '../model'\n\nconst noteStyle = {\n  position: 'absolute' as const,\n  left: 8,\n  top: 4,\n  zIndex: 5,\n  background: 'rgba(255,255,255,0.82)',\n  padding: '0 4px',\n  borderRadius: 3,\n}\n\nconst LinearGraphDisplay = observer(function LinearGraphDisplay({\n  model,\n}: {\n  model: LinearGraphDisplayModel\n}) {\n  const { pane, height } = model\n  return (\n    <div\n      data-testid=\"linear-graph-display\"\n      data-layout={pane.layoutMode}\n      data-cut-tier={pane.cutTier}\n      data-recuts={pane.recuts}\n      data-node-count={pane.hasGraph ? pane.nodeCount : undefined}\n      style={{\n        position: 'relative',\n        width: pane.width,\n        height,\n        overflow: 'hidden',\n      }}\n    >\n      <GraphCanvas model={pane} toolbar={false} />\n      {pane.hasGraph ? null : <GraphLoadStatus model={pane} />}\n      {pane.cutNote ? (\n        <Typography\n          variant=\"caption\"\n          color=\"warning.main\"\n          style={noteStyle}\n          data-testid=\"graph-cut-note\"\n        >\n          {pane.cutNote}\n        </Typography>\n      ) : null}\n    </div>\n  )\n})\n\nexport default LinearGraphDisplay\n"],
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c=a.get(u);c&&s.get(u)<l&&(d=Math.max(d,i.get(u)+c.length))}i.set(f.id,d)}return{offsets:i,ordered:o}}function Gt(e){let t=new Map(e.nodes.filter(ue).map(s=>[s.id,s])),n=fe(e),r=new Set,o=[];for(let s of t.values())if(s.stable.rank!==0&&!r.has(s.id)){let{members:a,anchors:i}=Zn(s.id,t,n,r),l=Qn(i);if(l){let{offsets:f,ordered:d}=tr(a,l.entry,n);o.push({start:l.start,refSpan:l.end-l.start,nodeIds:d.map(u=>u.id),nodeOffsets:d.map(u=>f.get(u.id)),pathLength:d.reduce((u,c)=>Math.max(u,f.get(c.id)+c.length),0)})}}return o.sort((s,a)=>s.start-a.start)}var nr=1,rr=.015;function Ee({graph:e,span:t,rowY:n,positions:r}){let o=trr,s=Gt(e),a=new Map(e.nodes.map(d=>[d.id,d])),i=[];for(let d of s){let u=d.refSpan-d.pathLength;u>=nr&&i.push({nodeIds:d.nodeIds,bp:u});let c=Math.max(d.refSpan,o),m=d.pathLength>0?c/d.pathLength:0;d.nodeIds.forEach((p,h)=>{let g=a.get(p);if(g){let b=d.nodeOffsets[h],y=c/d.nodeIds.length,N=M=>d.start+Mm,w=n(g);r[p]=m?[{x:N(b),y:w},{x:N(b+g.length),y:w}]:[{x:d.start+hy,y:w},{x:d.start+(h+1)y,y:w}]}})}let l=fe(e),f=Object.keys(r);for(let d of f){let u=r[d].at(-1).x;for(let c of l.get(d)??[]){let m=a.get(c);if(m&&!(c in r)){let p=n(m);r[c]=[{x:u,y:p},{x:u+o,y:p}],f.push(c)}}}return i}function or(e){let t=new Set;for(let n of e.nodes)n.stable&&t.add(n.stable.rank);return new Map([...t].sort((n,r)=>n-r).map((n,r)=>[n,r]))}function Ot(e,t){let n=F(e);if(n.length===0)return;let r=we(n,t),o=or(e),s=j(n),a=Ee({graph:e,span:r,rowY:l=>(l.stable?o.get(l.stable.rank)??o.size:o.size)20,positions:s}),i=[...o].map(([l,f])=>({label:l===0?"Reference (rank 0)":`Rank ${l}`,y:f20}));return{nodePositions:s,rowLabels:i,referenceAxis:!0,pixelRows:!0,alleleDeletions:a}}var sr=12,Ye=20;function _t(e){return 10+8Math.log2(1+e.length)}function K(e,t){return e<t?-1:e>t?1:0}function Tt(e,t){return K(e.at,t.at)\|\|K(e.side,t.side)\|\|K(e.hops,t.hops)}var Bt={at:1/0,side:0,hops:0};function ar(e){let t=new Map(e.nodes.map(r=>[r.id,r])),n=lr(e);return e.nodes.map(r=>r.id).sort((r,o)=>Tt(n.get(r)??Bt,n.get(o)??Bt)\|\|K(t.get(r).name,t.get(o).name)\|\|K(r,o))}function ir(e,t){let n=new Set(e.nodes.map(d=>d.id)),r=new Map(t.map(d=>[d.id,d.stable.start])),o=new Map,s=new Map;t.forEach((d,u)=>{s.set(d.id,t[u-1]?.id),o.set(d.id,t[u+1]?.id)});let a=t[0]?.id,i=(d,u)=>{let c=o.get(d);o.set(d,u),s.set(u,d),o.set(u,c),c!==void 0&&s.set(c,u)},l=(d,u)=>{let c=s.get(d);c===void 0?(a=u,s.set(u,void 0),o.set(u,d),s.set(d,u)):i(c,u)};for(let d of e.paths??[]){let u=0,c=0,m;for(let b of d.nodeIds){let y=r.get(b);y!==void 0&&(m!==void 0&&y!==m&&(y>m?u++:c++),m=y)}let p=c>u?[...d.nodeIds].reverse():d.nodeIds,h,g=new Set;for(let b of p)if(o.has(b)){if(h===void 0)for(let y of g)l(b,y);h=b}else n.has(b)&&(h===void 0?g.add(b):(i(h,b),h=b))}let f=[];for(let d=a;d!==void 0;d=o.get(d))f.push(d);return f}function cr(e,t){let n=[...t.entries()].sort(([a,i],[l,f])=>Tt(i,f)\|\|K(a,l)).map(([a])=>a),r=n.length;for(let a of n){let i=t.get(a);for(let l of e.get(a)??[])t.has(l)\|\|(t.set(l,{at:i.at,side:1,hops:i.hops+1}),n.push(l))}let o=new Set(n.slice(r)),s=new Set;for(let a of o){if(s.has(a))continue;let{at:i}=t.get(a),l=[a];s.add(a);let f=!0;for(let d of l){let{hops:u}=t.get(d),c=!0,m=!1;for(let p of e.get(d)??[]){let h=t.get(p);h.at===i&&o.has(p)?(c&&=h.hops<=u,s.has(p)\|\|(s.add(p),l.push(p))):h.at!==i&&(m\|\|=h.at<i,f&&=h.at<i)}f&&=!c\|\|m}if(f)for(let d of l){let u=t.get(d);t.set(d,{...u,side:-1,hops:-u.hops})}}}function lr(e){let t=new Set(e.nodes.map(s=>s.id)),n=new Map;for(let s of e.edges)!t.has(s.from)\|\|!t.has(s.to)\|\|((n.get(s.from)??n.set(s.from,[]).get(s.from)).push(s.to),(n.get(s.to)??n.set(s.to,[]).get(s.to)).push(s.from));let r=e.nodes.filter(S).sort((s,a)=>K(s.stable.start,a.stable.start)\|\|K(s.name,a.name)),o=new Map;return ir(e,r).forEach((s,a)=>{o.set(s,{at:a,side:0,hops:0})}),cr(n,o),o}function ur(e){let t=new Map(e.nodes.map(u=>[u.id,u])),n=ar(e),r=new Map(n.map((u,c)=>[u,c])),o=u=>S(t.get(u)),s=new Map(n.map(u=>[u,[]])),a=new Map(n.map(u=>[u,[]])),i=(u,c)=>{s.get(c).push(u),a.get(u).push(c)};for(let u of e.edges)u.from===u.to\|\|!r.has(u.from)\|\|!r.has(u.to)\|\|(r.get(u.from)<r.get(u.to)?i(u.from,u.to):i(u.to,u.from));let l=n.filter(o);for(let u=1;u<l.length;u++)i(l[u-1],l[u]);let f=new Map;for(let u of n){let c=0;for(let m of s.get(u))c=Math.max(c,f.get(m)+1);f.set(u,c)}for(let u=n.length-1;u>=0;u--){let c=n[u],m=a.get(c);if(o(c)\|\|m.length===0)continue;let p=1/0;for(let b of m)p=Math.min(p,f.get(b));let h=f.get(c),g=Math.max(h,p-1);f.set(c,Math.floor((h+g)/2))}let d=[];for(let u of n)(d[f.get(u)]??=[]).push(u);return{layers:d,layerOf:f,preds:s}}function Pt(e){if(!e.nodes.some(S))return;let t=new Map(e.nodes.map(u=>[u.id,u])),n=u=>S(t.get(u)),{layers:r,layerOf:o,preds:s}=ur(e),a=r.map(u=>{let c=0;for(let m of u)c=Math.max(c,_t(t.get(m)));return c}),i=[],l=0;for(let u=0;u<r.length;u++)i[u]=l,l+=a[u]+sr;let f=new Map;for(let u of r){let c=[];for(let p of u){if(n(p)){f.set(p,0);continue}let h=s.get(p).filter(b=>f.has(b)),g=0;for(let b of h)g+=f.get(b)/h.length;c.push({id:p,ideal:g===0?Ye:g})}c.sort((p,h)=>p.ideal-h.ideal);let m=new Set([0]);for(let{id:p,ideal:h}of c){let g=Math.round(h/Ye);g===0&&(g=h>=0?1:-1);for(let b=1;m.has(g);b++)m.has(g+b)?m.has(g-b)\|\|(g-=b):g+=b;m.add(g),f.set(p,gYe)}}let d={};for(let u of e.nodes){let c=o.get(u.id),m=_t(u),p=i[c]+a[c]/2,h=f.get(u.id);d[u.id]=[{x:p-m/2,y:h},{x:p+m/2,y:h}]}return{nodePositions:d,referenceAxis:!1,pixelRows:!0}}function dr(e,t){let n=new Map;for(let o of e.nodes)if(Ne(o)){let{sample:s}=Ce(o.stable.refName);n.set(s,(n.get(s)??0)+o.length)}let r=new Map(t.map((o,s)=>[o,s]));return[...n.keys()].sort((o,s)=>(r.get(o)??1/0)-(r.get(s)??1/0)\|\|n.get(s)-n.get(o)\|\|o.localeCompare(s))}function $t(e,t,n=[]){let r=F(e),o=dr(e,n);if(r.length===0\|\|o.length===0)return;let s=we(r,t),a=new Map(o.map((c,m)=>[c,m+1])),i=j(r),l=o.length+1,f=Ee({graph:e,span:s,rowY:c=>{let m=c.stable;return((m?a.get(Ce(m.refName).sample):void 0)??l)20},positions:i}),u=[{label:Ce(r[0].stable.refName).sample,y:0},...o.map(c=>({label:c,y:a.get(c)20}))];return{nodePositions:i,rowLabels:u,sampleRows:o,referenceAxis:!0,pixelRows:!0,alleleDeletions:f}}function Ht(e){let t=F(e);if(t.length!==0)return{nodePositions:j(t),referenceAxis:!0,pixelRows:!0}}var fr="Force-directed layout",U=e=>e.nodes.some(S),Dt=e=>U(e)&&(e.paths?.length??0)>1,zt=e=>U(e)&&e.nodes.some(Ne),Fe=[{value:"auto",label:"Anchored",description:"x is reference bp, one row per stable rank. 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